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Oligo Modifications List | Oligo Modifications Reference Category
Modification : Cy3.5
Reference Catalog Number 26-6461
Category Fluorescent Dyes
Modification Code Cy3.5
5 Prime Y
3 Prime Y
Internal Y
Molecular Weight (mw) 607.7
Extinction Coeficient (ec) 24
Technical Info (pdf) PS26-6461.pdf
Abvsorbance MAX 581
Emission MAX 596
Catalog NoScalePrice
26-6461-0550 nmol$660.00
26-6461-02200 nmol$660.00
26-6461-011 umol$858.00
26-6461-032 umol$1,287.00
26-6461-1010 umol$6,864.00
26-6461-1515 umol$8,580.00

Cyanine 3.5 (Cy3.5) is a fluorescent dye that belongs to the Cyanine family of synthetic polymethine dyes. Cy3.5 is reactive, water-soluble, and has an absorbance maximum of 581 nm and an emission maximum of 596 nm. It is available as a phosphoramidite, and is used to fluorescently label oligonucleotides at either the 5' or 3' end, or internally. Cy3.5 plays a particularly important role in real-time PCR applications, being used as a reporter moiety in TaqMan probes (1), Scorpion primers (2) and Molecular Beacons (3). For such probes, Cy3.5 is most commonly paired with the dark quencher BHQ-2, as the two have excellent spectral overlap.

Cy3 can also be used to label DNA oligos for use as hybridization probes in other applications, such as Fluorescent In-Situ Hybridization (FISH).

1. Livak, K.J., Flood, S.J.A., Marmaro, J., Giusti, W., Deetz, K. Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization.PCR Methods Appl. (1995), 4: 1-6.
2. Thelwell, N., Millington, S., Solinas, A., Booth, J., Brown, T. Mode of action and application of Scorpion primers to mutation detection. Nucleic Acids Res. (2000), 28: 3752-3761.
3. Tyagi, S., Kramer, F.R. Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. (1996), 14: 303-308.

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